Correlation between copy number variation genes (focal events) and molecular subtypes
Adrenocortical Carcinoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C15X27XP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C15X27XP
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 46 focal events and 10 molecular subtypes across 90 patients, 154 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- amp_4p16.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- amp_4q35.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- amp_5p15.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- amp_6p21.31 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

- amp_6q24.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- amp_7p22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_9q31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_12q14.1 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_14q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- amp_16p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- amp_16q22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- amp_16q24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- amp_17q25.3 cnv correlated to 'CN_CNMF'.

- amp_19p13.12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- amp_xp11.22 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

- amp_xq28 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_1p36.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_1q43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_2q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_2q37.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_3q13.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- del_4q34.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- del_7q36.3 cnv correlated to 'CN_CNMF'.

- del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- del_11q14.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- del_12q14.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- del_13q14.2 cnv correlated to 'CN_CNMF'.

- del_14q21.2 cnv correlated to 'CN_CNMF'.

- del_16p13.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- del_16q23.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_17q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_17q24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- del_18q21.2 cnv correlated to 'CN_CNMF'.

- del_20p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- del_22q12.1 cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 46 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 154 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
amp 14q11 2 | 27 (30%) | 63 | 7e-05 (0.00189) | 0.0136 (0.063) | 0.00942 (0.0498) | 0.0291 (0.105) | 6e-05 (0.00184) | 1e-05 (0.000354) | 0.00026 (0.00517) | 0.00686 (0.0429) | 0.00078 (0.0112) | 0.00119 (0.0134)
amp 5q35 3 | 63 (70%) | 27 | 1e-05 (0.000354) | 0.00141 (0.0147) | 0.503 (0.676) | 0.00671 (0.0429) | 1e-05 (0.000354) | 1e-05 (0.000354) | 0.00648 (0.0426) | 0.0466 (0.141) | 0.0118 (0.0566) | 0.291 (0.488)
amp 16q24 2 | 49 (54%) | 41 | 1e-05 (0.000354) | 0.0279 (0.103) | 1 (1.00) | 0.324 (0.509) | 0.00027 (0.00517) | 1e-05 (0.000354) | 0.0621 (0.174) | 0.00239 (0.0207) | 0.00555 (0.0393) | 0.381 (0.567)
del 4q34 3 | 25 (28%) | 65 | 0.00134 (0.0143) | 0.0645 (0.18) | 0.729 (0.844) | 0.638 (0.767) | 0.0215 (0.0862) | 0.0388 (0.129) | 0.0365 (0.123) | 0.0424 (0.134) | 7e-05 (0.00189) | 0.248 (0.443)
del 9p23 | 24 (27%) | 66 | 0.00907 (0.0497) | 0.00828 (0.0478) | 0.0549 (0.157) | 0.0509 (0.151) | 4e-05 (0.00131) | 0.00124 (0.0136) | 0.00769 (0.0459) | 0.174 (0.366) | 0.00832 (0.0478) | 0.735 (0.845)
del 9p21 3 | 27 (30%) | 63 | 0.0069 (0.0429) | 0.0035 (0.0293) | 0.0682 (0.184) | 0.228 (0.425) | 1e-05 (0.000354) | 0.00033 (0.00607) | 0.0165 (0.0725) | 0.182 (0.372) | 0.00934 (0.0498) | 0.567 (0.713)
amp 1q22 | 17 (19%) | 73 | 0.00812 (0.0478) | 0.00036 (0.00637) | 1 (1.00) | 0.401 (0.584) | 0.00225 (0.0202) | 0.00026 (0.00517) | 0.116 (0.277) | 0.155 (0.339) | 0.0144 (0.0657) | 0.441 (0.632)
amp 5p15 33 | 65 (72%) | 25 | 1e-05 (0.000354) | 0.886 (0.943) | 0.729 (0.844) | 0.89 (0.946) | 0.00966 (0.0499) | 0.00093 (0.0119) | 0.0444 (0.138) | 0.179 (0.37) | 0.015 (0.067) | 0.307 (0.499)
amp 9q31 3 | 34 (38%) | 56 | 0.00057 (0.00874) | 0.0203 (0.0825) | 0.0113 (0.0551) | 0.138 (0.317) | 0.0291 (0.105) | 0.0181 (0.077) | 0.0547 (0.157) | 0.2 (0.385) | 0.248 (0.443) | 0.128 (0.299)
amp 19p13 12 | 58 (64%) | 32 | 0.00041 (0.0065) | 0.0342 (0.117) | 0.323 (0.509) | 0.0105 (0.0533) | 0.00198 (0.0182) | 0.0004 (0.0065) | 0.326 (0.509) | 0.481 (0.667) | 0.582 (0.725) | 0.174 (0.366)
amp xq28 | 46 (51%) | 44 | 0.0004 (0.0065) | 0.755 (0.851) | 0.223 (0.417) | 0.0445 (0.138) | 0.0089 (0.0493) | 0.0114 (0.0551) | 0.512 (0.679) | 0.26 (0.451) | 1 (1.00) | 0.0297 (0.106)
del 17q21 31 | 26 (29%) | 64 | 0.00408 (0.0321) | 0.00939 (0.0498) | 0.0682 (0.184) | 0.542 (0.702) | 0.0747 (0.2) | 0.0461 (0.14) | 0.036 (0.122) | 0.00522 (0.0375) | 0.185 (0.375) | 0.0612 (0.173)
del 20p12 1 | 12 (13%) | 78 | 0.00472 (0.0356) | 0.64 (0.767) | 0.352 (0.536) | 0.621 (0.756) | 0.0424 (0.134) | 0.0273 (0.101) | 0.00626 (0.0417) | 0.514 (0.679) | 0.00159 (0.0161) | 1 (1.00)
amp 4p16 3 | 41 (46%) | 49 | 0.00098 (0.0119) | 0.548 (0.705) | 1 (1.00) | 0.192 (0.377) | 0.0131 (0.0614) | 0.0059 (0.0405) | 0.485 (0.668) | 0.0471 (0.142) | 0.406 (0.584) | 0.952 (0.989)
amp 4q35 1 | 29 (32%) | 61 | 1e-05 (0.000354) | 0.196 (0.382) | 0.767 (0.852) | 0.557 (0.707) | 0.00068 (0.0101) | 0.00093 (0.0119) | 0.0546 (0.157) | 0.00106 (0.0125) | 0.0673 (0.184) | 0.292 (0.488)
amp 12q14 1 | 70 (78%) | 20 | 1e-05 (0.000354) | 0.282 (0.48) | 0.143 (0.321) | 0.0104 (0.0532) | 0.0221 (0.0867) | 0.00191 (0.0182) | 0.458 (0.652) | 0.487 (0.669) | 0.35 (0.536) | 0.0885 (0.228)
amp 16p13 3 | 50 (56%) | 40 | 1e-05 (0.000354) | 0.259 (0.451) | 0.769 (0.852) | 0.0517 (0.152) | 0.00025 (0.00517) | 1e-05 (0.000354) | 0.0759 (0.202) | 0.00958 (0.0499) | 0.0532 (0.155) | 0.586 (0.726)
amp 16q22 1 | 56 (62%) | 34 | 1e-05 (0.000354) | 0.369 (0.551) | 0.546 (0.705) | 0.802 (0.88) | 0.0294 (0.106) | 0.00014 (0.00322) | 0.0659 (0.181) | 0.0225 (0.0876) | 0.155 (0.339) | 0.861 (0.922)
amp 19q12 | 56 (62%) | 34 | 0.00098 (0.0119) | 0.0203 (0.0825) | 0.369 (0.551) | 0.166 (0.354) | 0.00188 (0.0182) | 0.00112 (0.0129) | 0.197 (0.382) | 0.255 (0.449) | 0.514 (0.679) | 0.061 (0.173)
del 4q35 1 | 30 (33%) | 60 | 0.00571 (0.0398) | 0.0123 (0.0583) | 0.528 (0.692) | 0.391 (0.581) | 0.0978 (0.242) | 0.0415 (0.133) | 0.193 (0.377) | 0.167 (0.355) | 0.00092 (0.0119) | 0.684 (0.805)
del 16q23 1 | 11 (12%) | 79 | 0.00856 (0.048) | 0.506 (0.677) | 0.193 (0.377) | 0.232 (0.428) | 0.0416 (0.133) | 0.0107 (0.0537) | 0.272 (0.467) | 0.136 (0.315) | 0.0111 (0.0551) | 0.541 (0.702)
del 17q24 2 | 24 (27%) | 66 | 0.00195 (0.0182) | 0.0148 (0.0668) | 0.205 (0.389) | 0.293 (0.488) | 0.16 (0.342) | 0.0412 (0.133) | 0.156 (0.339) | 0.026 (0.0981) | 0.0519 (0.152) | 0.238 (0.432)
amp 7p22 1 | 54 (60%) | 36 | 0.00228 (0.0202) | 0.483 (0.667) | 0.746 (0.845) | 0.674 (0.795) | 0.00726 (0.0445) | 0.0324 (0.114) | 0.567 (0.713) | 0.492 (0.673) | 0.805 (0.882) | 0.134 (0.312)
amp xp11 22 | 49 (54%) | 41 | 0.0001 (0.00256) | 0.92 (0.964) | 0.765 (0.852) | 0.0168 (0.0727) | 0.0333 (0.116) | 0.0968 (0.241) | 0.762 (0.851) | 0.143 (0.321) | 0.741 (0.845) | 0.0884 (0.228)
del 1p36 23 | 38 (42%) | 52 | 0.0217 (0.0862) | 0.00417 (0.0321) | 0.366 (0.551) | 0.149 (0.331) | 0.0718 (0.193) | 0.00364 (0.0294) | 0.835 (0.904) | 0.56 (0.708) | 0.401 (0.584) | 0.823 (0.899)
del 4q34 3 | 28 (31%) | 62 | 0.00161 (0.0161) | 0.00494 (0.0367) | 0.759 (0.851) | 0.145 (0.324) | 0.186 (0.375) | 0.187 (0.376) | 0.0897 (0.228) | 0.189 (0.377) | 0.00011 (0.00266) | 0.265 (0.458)
del 11p15 5 | 27 (30%) | 63 | 0.00767 (0.0459) | 0.0204 (0.0825) | 0.746 (0.845) | 0.673 (0.795) | 0.0894 (0.228) | 0.0338 (0.117) | 0.124 (0.291) | 0.598 (0.732) | 0.393 (0.581) | 0.514 (0.679)
del 16p13 3 | 7 (8%) | 83 | 0.0806 (0.212) | 0.558 (0.707) | 0.396 (0.581) | 0.342 (0.527) | 0.541 (0.702) | 0.00841 (0.0478) | 0.0238 (0.0911) | 0.598 (0.732) | 0.0199 (0.0825) | 0.76 (0.851)
del 17q11 2 | 24 (27%) | 66 | 0.0154 (0.0681) | 0.00507 (0.037) | 0.205 (0.389) | 0.63 (0.763) | 0.104 (0.253) | 0.105 (0.253) | 0.259 (0.451) | 0.018 (0.077) | 0.111 (0.268) | 0.396 (0.581)
amp 6q24 3 | 19 (21%) | 71 | 0.0234 (0.0903) | 0.909 (0.961) | 0.503 (0.676) | 0.639 (0.767) | 0.0478 (0.143) | 0.935 (0.975) | 0.67 (0.795) | 0.229 (0.425) | 0.632 (0.764) | 1 (1.00)
del 1q43 | 18 (20%) | 72 | 0.0141 (0.065) | 0.0451 (0.139) | 0.193 (0.377) | 0.159 (0.342) | 0.585 (0.726) | 0.138 (0.317) | 0.524 (0.69) | 0.553 (0.707) | 0.192 (0.377) | 0.181 (0.371)
del 2q22 1 | 18 (20%) | 72 | 0.0398 (0.13) | 0.00362 (0.0294) | 0.476 (0.666) | 0.794 (0.878) | 0.24 (0.432) | 0.0892 (0.228) | 0.314 (0.505) | 0.664 (0.792) | 0.406 (0.584) | 0.493 (0.673)
del 2q37 3 | 21 (23%) | 69 | 0.00622 (0.0417) | 0.0257 (0.0977) | 0.729 (0.844) | 0.831 (0.901) | 0.3 (0.494) | 0.0918 (0.231) | 0.482 (0.667) | 0.526 (0.691) | 0.569 (0.713) | 0.938 (0.976)
del 3q13 31 | 25 (28%) | 65 | 0.299 (0.494) | 0.0461 (0.14) | 0.177 (0.367) | 0.472 (0.662) | 0.157 (0.34) | 0.0398 (0.13) | 0.453 (0.648) | 0.2 (0.385) | 0.852 (0.917) | 0.368 (0.551)
del 11q14 1 | 25 (28%) | 65 | 0.0193 (0.0814) | 0.00681 (0.0429) | 0.503 (0.676) | 0.551 (0.705) | 0.218 (0.413) | 0.352 (0.536) | 0.28 (0.479) | 0.745 (0.845) | 0.324 (0.509) | 0.587 (0.726)
amp 6p21 31 | 19 (21%) | 71 | 0.065 (0.18) | 0.8 (0.88) | 0.705 (0.823) | 0.8 (0.88) | 0.0798 (0.211) | 1 (1.00) | 0.14 (0.318) | 0.0263 (0.0982) | 0.405 (0.584) | 0.301 (0.494)
amp 17q25 3 | 18 (20%) | 72 | 0.0346 (0.118) | 0.688 (0.808) | 0.469 (0.66) | 0.1 (0.246) | 0.123 (0.291) | 0.674 (0.795) | 0.4 (0.584) | 0.693 (0.811) | 0.309 (0.499) | 0.468 (0.66)
del 7q36 3 | 11 (12%) | 79 | 0.038 (0.127) | 0.252 (0.448) | 0.236 (0.432) | 0.664 (0.792) | 0.177 (0.367) | 0.338 (0.523) | 0.895 (0.949) | 0.737 (0.845) | 0.0963 (0.241) | 0.246 (0.442)
del 12q14 2 | 5 (6%) | 85 | 0.0907 (0.229) | 0.222 (0.417) | 1 (1.00) |  | 0.177 (0.367) | 0.00091 (0.0119) | 0.594 (0.732) | 0.305 (0.498) | 0.853 (0.917) | 0.149 (0.331)
del 13q14 2 | 42 (47%) | 48 | 0.00327 (0.0279) | 0.0877 (0.228) | 0.55 (0.705) | 0.841 (0.909) | 0.333 (0.517) | 0.556 (0.707) | 1 (1.00) | 0.532 (0.695) | 0.404 (0.584) | 0.826 (0.899)
del 14q21 2 | 20 (22%) | 70 | 0.0199 (0.0825) | 0.924 (0.966) | 0.73 (0.844) | 0.581 (0.725) | 0.303 (0.496) | 0.284 (0.483) | 0.369 (0.551) | 0.733 (0.845) | 0.27 (0.465) | 0.158 (0.341)
del 18q21 2 | 36 (40%) | 54 | 0.0314 (0.111) | 0.319 (0.507) | 0.759 (0.851) | 0.326 (0.509) | 0.824 (0.899) | 1 (1.00) | 0.496 (0.675) | 0.914 (0.964) | 0.291 (0.488) | 0.353 (0.536)
del 22q12 1 | 50 (56%) | 40 | 0.00419 (0.0321) | 0.139 (0.317) | 0.233 (0.429) | 0.294 (0.489) | 0.748 (0.845) | 0.185 (0.375) | 0.63 (0.763) | 0.879 (0.938) | 0.917 (0.964) | 0.203 (0.389)
del 6p24 3 | 20 (22%) | 70 | 0.112 (0.269) | 0.92 (0.964) | 0.469 (0.66) | 0.317 (0.507) | 0.621 (0.756) | 0.481 (0.667) | 1 (1.00) | 0.1 (0.246) | 1 (1.00) | 0.46 (0.652)
del 6q26 | 21 (23%) | 69 | 0.118 (0.28) | 0.862 (0.922) | 0.503 (0.676) | 0.317 (0.507) | 0.32 (0.508) | 0.309 (0.499) | 0.505 (0.677) | 0.349 (0.536) | 0.223 (0.417) | 0.596 (0.732)
del 10q23 1 | 11 (12%) | 79 | 0.255 (0.449) | 0.259 (0.451) | 1 (1.00) | 0.239 (0.432) | 0.239 (0.432) | 0.745 (0.845) | 1 (1.00) | 0.969 (1.00) | 1 (1.00) | 0.287 (0.485)

'amp_1q22' versus 'CN_CNMF'

P value = 0.00812 (Fisher's exact test), Q value = 0.048

Table S1. Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 1(1Q22) MUTATED | 13 | 2 | 2 | 0
AMP PEAK 1(1Q22) WILD-TYPE | 23 | 24 | 14 | 12

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0064

Table S2. Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
AMP PEAK 1(1Q22) MUTATED | 9 | 2 | 0 | 4 | 0
AMP PEAK 1(1Q22) WILD-TYPE | 9 | 9 | 20 | 14 | 11

Figure S2. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.02

Table S3. Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 1(1Q22) MUTATED | 11 | 1 | 1 | 2
AMP PEAK 1(1Q22) WILD-TYPE | 13 | 12 | 16 | 21

Figure S3. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0052

Table S4. Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 1(1Q22) MUTATED | 11 | 1 | 2 | 1
AMP PEAK 1(1Q22) WILD-TYPE | 12 | 22 | 5 | 23

Figure S4. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.066

Table S5. Gene #1: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
AMP PEAK 1(1Q22) MUTATED | 4 | 9 | 2
AMP PEAK 1(1Q22) WILD-TYPE | 24 | 13 | 25

Figure S5. Get High-res Image Gene #1: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.012

Table S6. Gene #2: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 2(4P16.3) MUTATED | 8 | 13 | 11 | 9
AMP PEAK 2(4P16.3) WILD-TYPE | 28 | 13 | 5 | 3

Figure S6. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.061

Table S7. Gene #2: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 2(4P16.3) MUTATED | 5 | 7 | 12 | 10
AMP PEAK 2(4P16.3) WILD-TYPE | 19 | 6 | 5 | 13

Figure S7. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0059 (Fisher's exact test), Q value = 0.041

Table S8. Gene #2: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 2(4P16.3) MUTATED | 5 | 15 | 1 | 13
AMP PEAK 2(4P16.3) WILD-TYPE | 18 | 8 | 6 | 11

Figure S8. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.14

Table S9. Gene #2: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 2(4P16.3) MUTATED | 11 | 10 | 6 | 5 | 3
AMP PEAK 2(4P16.3) WILD-TYPE | 5 | 17 | 5 | 15 | 1

Figure S9. Get High-res Image Gene #2: 'amp_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S10. Gene #3: 'amp_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 3(4Q35.1) MUTATED | 2 | 10 | 7 | 10
AMP PEAK 3(4Q35.1) WILD-TYPE | 34 | 16 | 9 | 2

Figure S10. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.01

Table S11. Gene #3: 'amp_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 3(4Q35.1) MUTATED | 1 | 4 | 9 | 11
AMP PEAK 3(4Q35.1) WILD-TYPE | 23 | 9 | 8 | 12

Figure S11. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.012

Table S12. Gene #3: 'amp_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 3(4Q35.1) MUTATED | 2 | 10 | 0 | 13
AMP PEAK 3(4Q35.1) WILD-TYPE | 21 | 13 | 7 | 11

Figure S12. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.013

Table S13. Gene #3: 'amp_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 3(4Q35.1) MUTATED | 7 | 10 | 6 | 0 | 2
AMP PEAK 3(4Q35.1) WILD-TYPE | 9 | 17 | 5 | 20 | 2

Figure S13. Get High-res Image Gene #3: 'amp_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S14. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 4(5P15.33) MUTATED | 14 | 25 | 15 | 11
AMP PEAK 4(5P15.33) WILD-TYPE | 22 | 1 | 1 | 1

Figure S14. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 0.05

Table S15. Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 4(5P15.33) MUTATED | 12 | 10 | 16 | 19
AMP PEAK 4(5P15.33) WILD-TYPE | 12 | 3 | 1 | 4

Figure S15. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.012

Table S16. Gene #4: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 4(5P15.33) MUTATED | 13 | 20 | 2 | 22
AMP PEAK 4(5P15.33) WILD-TYPE | 10 | 3 | 5 | 2

Figure S16. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.14

Table S17. Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
AMP PEAK 4(5P15.33) MUTATED | 28 | 8 | 22
AMP PEAK 4(5P15.33) WILD-TYPE | 8 | 8 | 4

Figure S17. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.067

Table S18. Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
AMP PEAK 4(5P15.33) MUTATED | 23 | 11 | 23
AMP PEAK 4(5P15.33) WILD-TYPE | 5 | 11 | 4

Figure S18. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S19. Gene #5: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 5(5Q35.3) MUTATED | 12 | 26 | 15 | 10
AMP PEAK 5(5Q35.3) WILD-TYPE | 24 | 0 | 1 | 2

Figure S19. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.015

Table S20. Gene #5: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
AMP PEAK 5(5Q35.3) MUTATED | 7 | 7 | 19 | 13 | 10
AMP PEAK 5(5Q35.3) WILD-TYPE | 11 | 4 | 1 | 5 | 1

Figure S20. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00671 (Fisher's exact test), Q value = 0.043

Table S21. Gene #5: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
AMP PEAK 5(5Q35.3) MUTATED | 4 | 7 | 7 | 1 | 2 | 4 | 6 | 3
AMP PEAK 5(5Q35.3) WILD-TYPE | 4 | 0 | 0 | 2 | 2 | 0 | 0 | 3

Figure S21. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S22. Gene #5: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 5(5Q35.3) MUTATED | 7 | 12 | 16 | 20
AMP PEAK 5(5Q35.3) WILD-TYPE | 17 | 1 | 1 | 3

Figure S22. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S23. Gene #5: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 5(5Q35.3) MUTATED | 8 | 22 | 2 | 23
AMP PEAK 5(5Q35.3) WILD-TYPE | 15 | 1 | 5 | 1

Figure S23. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.043

Table S24. Gene #5: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
AMP PEAK 5(5Q35.3) MUTATED | 24 | 8 | 24
AMP PEAK 5(5Q35.3) WILD-TYPE | 12 | 8 | 2

Figure S24. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.14

Table S25. Gene #5: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 5(5Q35.3) MUTATED | 14 | 21 | 9 | 9 | 3
AMP PEAK 5(5Q35.3) WILD-TYPE | 2 | 6 | 2 | 11 | 1

Figure S25. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.057

Table S26. Gene #5: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
AMP PEAK 5(5Q35.3) MUTATED | 20 | 11 | 24
AMP PEAK 5(5Q35.3) WILD-TYPE | 8 | 11 | 3

Figure S26. Get High-res Image Gene #5: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.098

Table S27. Gene #6: 'amp_6p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 6(6P21.31) MUTATED | 5 | 2 | 5 | 2 | 0
AMP PEAK 6(6P21.31) WILD-TYPE | 11 | 25 | 6 | 18 | 4

Figure S27. Get High-res Image Gene #6: 'amp_6p21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'CN_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.09

Table S28. Gene #7: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 7(6Q24.3) MUTATED | 9 | 1 | 4 | 5
AMP PEAK 7(6Q24.3) WILD-TYPE | 27 | 25 | 12 | 7

Figure S28. Get High-res Image Gene #7: 'amp_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.14

Table S29. Gene #7: 'amp_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 7(6Q24.3) MUTATED | 5 | 0 | 7 | 4
AMP PEAK 7(6Q24.3) WILD-TYPE | 19 | 13 | 10 | 19

Figure S29. Get High-res Image Gene #7: 'amp_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'CN_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.02

Table S30. Gene #8: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 8(7P22.1) MUTATED | 13 | 20 | 13 | 8
AMP PEAK 8(7P22.1) WILD-TYPE | 23 | 6 | 3 | 4

Figure S30. Get High-res Image Gene #8: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00726 (Fisher's exact test), Q value = 0.045

Table S31. Gene #8: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 8(7P22.1) MUTATED | 10 | 12 | 13 | 12
AMP PEAK 8(7P22.1) WILD-TYPE | 14 | 1 | 4 | 11

Figure S31. Get High-res Image Gene #8: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.11

Table S32. Gene #8: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 8(7P22.1) MUTATED | 12 | 19 | 2 | 14
AMP PEAK 8(7P22.1) WILD-TYPE | 11 | 4 | 5 | 10

Figure S32. Get High-res Image Gene #8: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q31.3' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0087

Table S33. Gene #9: 'amp_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 9(9Q31.3) MUTATED | 11 | 5 | 13 | 5
AMP PEAK 9(9Q31.3) WILD-TYPE | 25 | 21 | 3 | 7

Figure S33. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q31.3' versus 'METHLYATION_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.082

Table S34. Gene #9: 'amp_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
AMP PEAK 9(9Q31.3) MUTATED | 9 | 5 | 9 | 2 | 1
AMP PEAK 9(9Q31.3) WILD-TYPE | 9 | 6 | 11 | 16 | 10

Figure S34. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q31.3' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.055

Table S35. Gene #9: 'amp_9q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
AMP PEAK 9(9Q31.3) MUTATED | 3 | 13
AMP PEAK 9(9Q31.3) WILD-TYPE | 18 | 11

Figure S35. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_9q31.3' versus 'MRNASEQ_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.11

Table S36. Gene #9: 'amp_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 9(9Q31.3) MUTATED | 8 | 8 | 6 | 3
AMP PEAK 9(9Q31.3) WILD-TYPE | 16 | 5 | 11 | 20

Figure S36. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.077

Table S37. Gene #9: 'amp_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 9(9Q31.3) MUTATED | 9 | 12 | 1 | 3
AMP PEAK 9(9Q31.3) WILD-TYPE | 14 | 11 | 6 | 21

Figure S37. Get High-res Image Gene #9: 'amp_9q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S38. Gene #10: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 10(12Q14.1) MUTATED | 19 | 26 | 16 | 9
AMP PEAK 10(12Q14.1) WILD-TYPE | 17 | 0 | 0 | 3

Figure S38. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.053

Table S39. Gene #10: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
AMP PEAK 10(12Q14.1) MUTATED | 7 | 6 | 7 | 3 | 3 | 4 | 5 | 1
AMP PEAK 10(12Q14.1) WILD-TYPE | 1 | 1 | 0 | 0 | 1 | 0 | 1 | 5

Figure S39. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.087

Table S40. Gene #10: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 10(12Q14.1) MUTATED | 14 | 13 | 14 | 19
AMP PEAK 10(12Q14.1) WILD-TYPE | 10 | 0 | 3 | 4

Figure S40. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.018

Table S41. Gene #10: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 10(12Q14.1) MUTATED | 14 | 20 | 3 | 23
AMP PEAK 10(12Q14.1) WILD-TYPE | 9 | 3 | 4 | 1

Figure S41. Get High-res Image Gene #10: 'amp_12q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0019

Table S42. Gene #11: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 11(14Q11.2) MUTATED | 7 | 5 | 13 | 2
AMP PEAK 11(14Q11.2) WILD-TYPE | 29 | 21 | 3 | 10

Figure S42. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.063

Table S43. Gene #11: 'amp_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
AMP PEAK 11(14Q11.2) MUTATED | 6 | 4 | 11 | 1 | 2
AMP PEAK 11(14Q11.2) WILD-TYPE | 12 | 7 | 9 | 17 | 9

Figure S43. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q11.2' versus 'RPPA_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.05

Table S44. Gene #11: 'amp_14q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
AMP PEAK 11(14Q11.2) MUTATED | 2 | 11
AMP PEAK 11(14Q11.2) WILD-TYPE | 19 | 13

Figure S44. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_14q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.11

Table S45. Gene #11: 'amp_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
AMP PEAK 11(14Q11.2) MUTATED | 3 | 5 | 0 | 2 | 0 | 0 | 1 | 2
AMP PEAK 11(14Q11.2) WILD-TYPE | 5 | 2 | 7 | 1 | 4 | 4 | 5 | 4

Figure S45. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_14q11.2' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0018

Table S46. Gene #11: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 11(14Q11.2) MUTATED | 4 | 7 | 11 | 1
AMP PEAK 11(14Q11.2) WILD-TYPE | 20 | 6 | 6 | 22

Figure S46. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S47. Gene #11: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 11(14Q11.2) MUTATED | 5 | 16 | 0 | 2
AMP PEAK 11(14Q11.2) WILD-TYPE | 18 | 7 | 7 | 22

Figure S47. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0052

Table S48. Gene #11: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
AMP PEAK 11(14Q11.2) MUTATED | 19 | 3 | 2
AMP PEAK 11(14Q11.2) WILD-TYPE | 17 | 13 | 24

Figure S48. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00686 (Fisher's exact test), Q value = 0.043

Table S49. Gene #11: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 11(14Q11.2) MUTATED | 9 | 3 | 3 | 6 | 3
AMP PEAK 11(14Q11.2) WILD-TYPE | 7 | 24 | 8 | 14 | 1

Figure S49. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.011

Table S50. Gene #11: 'amp_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
AMP PEAK 11(14Q11.2) MUTATED | 15 | 6 | 2
AMP PEAK 11(14Q11.2) WILD-TYPE | 13 | 16 | 25

Figure S50. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.013

Table S51. Gene #11: 'amp_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
AMP PEAK 11(14Q11.2) MUTATED | 19 | 3 | 1
AMP PEAK 11(14Q11.2) WILD-TYPE | 20 | 21 | 13

Figure S51. Get High-res Image Gene #11: 'amp_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S52. Gene #12: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 12(16P13.3) MUTATED | 6 | 26 | 11 | 7
AMP PEAK 12(16P13.3) WILD-TYPE | 30 | 0 | 5 | 5

Figure S52. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0052

Table S53. Gene #12: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 12(16P13.3) MUTATED | 5 | 9 | 14 | 16
AMP PEAK 12(16P13.3) WILD-TYPE | 19 | 4 | 3 | 7

Figure S53. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S54. Gene #12: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 12(16P13.3) MUTATED | 6 | 19 | 0 | 19
AMP PEAK 12(16P13.3) WILD-TYPE | 17 | 4 | 7 | 5

Figure S54. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00958 (Fisher's exact test), Q value = 0.05

Table S55. Gene #12: 'amp_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 12(16P13.3) MUTATED | 14 | 16 | 7 | 6 | 2
AMP PEAK 12(16P13.3) WILD-TYPE | 2 | 11 | 4 | 14 | 2

Figure S55. Get High-res Image Gene #12: 'amp_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S56. Gene #13: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 13(16Q22.1) MUTATED | 10 | 26 | 14 | 6
AMP PEAK 13(16Q22.1) WILD-TYPE | 26 | 0 | 2 | 6

Figure S56. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.11

Table S57. Gene #13: 'amp_16q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 13(16Q22.1) MUTATED | 9 | 10 | 13 | 16
AMP PEAK 13(16Q22.1) WILD-TYPE | 15 | 3 | 4 | 7

Figure S57. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0032

Table S58. Gene #13: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 13(16Q22.1) MUTATED | 9 | 20 | 1 | 18
AMP PEAK 13(16Q22.1) WILD-TYPE | 14 | 3 | 6 | 6

Figure S58. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.088

Table S59. Gene #13: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 13(16Q22.1) MUTATED | 15 | 17 | 6 | 9 | 2
AMP PEAK 13(16Q22.1) WILD-TYPE | 1 | 10 | 5 | 11 | 2

Figure S59. Get High-res Image Gene #13: 'amp_16q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S60. Gene #14: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 14(16Q24.2) MUTATED | 6 | 26 | 11 | 6
AMP PEAK 14(16Q24.2) WILD-TYPE | 30 | 0 | 5 | 6

Figure S60. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_16q24.2' versus 'METHLYATION_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.1

Table S61. Gene #14: 'amp_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
AMP PEAK 14(16Q24.2) MUTATED | 5 | 6 | 16 | 11 | 6
AMP PEAK 14(16Q24.2) WILD-TYPE | 13 | 5 | 4 | 7 | 5

Figure S61. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0052

Table S62. Gene #14: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 14(16Q24.2) MUTATED | 5 | 10 | 13 | 16
AMP PEAK 14(16Q24.2) WILD-TYPE | 19 | 3 | 4 | 7

Figure S62. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_16q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S63. Gene #14: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 14(16Q24.2) MUTATED | 5 | 20 | 1 | 18
AMP PEAK 14(16Q24.2) WILD-TYPE | 18 | 3 | 6 | 6

Figure S63. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.021

Table S64. Gene #14: 'amp_16q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
AMP PEAK 14(16Q24.2) MUTATED | 14 | 17 | 6 | 5 | 2
AMP PEAK 14(16Q24.2) WILD-TYPE | 2 | 10 | 5 | 15 | 2

Figure S64. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.039

Table S65. Gene #14: 'amp_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
AMP PEAK 14(16Q24.2) MUTATED | 18 | 6 | 19
AMP PEAK 14(16Q24.2) WILD-TYPE | 10 | 16 | 8

Figure S65. Get High-res Image Gene #14: 'amp_16q24.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.12

Table S66. Gene #15: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 15(17Q25.3) MUTATED | 12 | 2 | 1 | 3
AMP PEAK 15(17Q25.3) WILD-TYPE | 24 | 24 | 15 | 9

Figure S66. Get High-res Image Gene #15: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0065

Table S67. Gene #16: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 16(19P13.12) MUTATED | 16 | 17 | 16 | 9
AMP PEAK 16(19P13.12) WILD-TYPE | 20 | 9 | 0 | 3

Figure S67. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.12

Table S68. Gene #16: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
AMP PEAK 16(19P13.12) MUTATED | 14 | 8 | 16 | 7 | 5
AMP PEAK 16(19P13.12) WILD-TYPE | 4 | 3 | 4 | 11 | 6

Figure S68. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.053

Table S69. Gene #16: 'amp_19p13.12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
AMP PEAK 16(19P13.12) MUTATED | 8 | 7 | 4 | 3 | 1 | 3 | 4 | 2
AMP PEAK 16(19P13.12) WILD-TYPE | 0 | 0 | 3 | 0 | 3 | 1 | 2 | 4

Figure S69. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.018

Table S70. Gene #16: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 16(19P13.12) MUTATED | 12 | 13 | 13 | 11
AMP PEAK 16(19P13.12) WILD-TYPE | 12 | 0 | 4 | 12

Figure S70. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0065

Table S71. Gene #16: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 16(19P13.12) MUTATED | 15 | 21 | 1 | 12
AMP PEAK 16(19P13.12) WILD-TYPE | 8 | 2 | 6 | 12

Figure S71. Get High-res Image Gene #16: 'amp_19p13.12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.012

Table S72. Gene #17: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 17(19Q12) MUTATED | 17 | 15 | 16 | 8
AMP PEAK 17(19Q12) WILD-TYPE | 19 | 11 | 0 | 4

Figure S72. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.082

Table S73. Gene #17: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
AMP PEAK 17(19Q12) MUTATED | 14 | 7 | 16 | 7 | 4
AMP PEAK 17(19Q12) WILD-TYPE | 4 | 4 | 4 | 11 | 7

Figure S73. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.018

Table S74. Gene #17: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 17(19Q12) MUTATED | 12 | 13 | 12 | 10
AMP PEAK 17(19Q12) WILD-TYPE | 12 | 0 | 5 | 13

Figure S74. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.013

Table S75. Gene #17: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 17(19Q12) MUTATED | 15 | 20 | 1 | 11
AMP PEAK 17(19Q12) WILD-TYPE | 8 | 3 | 6 | 13

Figure S75. Get High-res Image Gene #17: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.22' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0026

Table S76. Gene #18: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 18(XP11.22) MUTATED | 11 | 22 | 11 | 5
AMP PEAK 18(XP11.22) WILD-TYPE | 25 | 4 | 5 | 7

Figure S76. Get High-res Image Gene #18: 'amp_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.073

Table S77. Gene #18: 'amp_xp11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
AMP PEAK 18(XP11.22) MUTATED | 7 | 6 | 5 | 1 | 3 | 3 | 4 | 0
AMP PEAK 18(XP11.22) WILD-TYPE | 1 | 1 | 2 | 2 | 1 | 1 | 2 | 6

Figure S77. Get High-res Image Gene #18: 'amp_xp11.22' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xp11.22' versus 'MRNASEQ_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.12

Table S78. Gene #18: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 18(XP11.22) MUTATED | 8 | 10 | 12 | 12
AMP PEAK 18(XP11.22) WILD-TYPE | 16 | 3 | 5 | 11

Figure S78. Get High-res Image Gene #18: 'amp_xp11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0065

Table S79. Gene #19: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
AMP PEAK 19(XQ28) MUTATED | 10 | 21 | 9 | 6
AMP PEAK 19(XQ28) WILD-TYPE | 26 | 5 | 7 | 6

Figure S79. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'RPPA_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.14

Table S80. Gene #19: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
AMP PEAK 19(XQ28) MUTATED | 6 | 5 | 6 | 1 | 2 | 3 | 4 | 0
AMP PEAK 19(XQ28) WILD-TYPE | 2 | 2 | 1 | 2 | 2 | 1 | 2 | 6

Figure S80. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.0089 (Fisher's exact test), Q value = 0.049

Table S81. Gene #19: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
AMP PEAK 19(XQ28) MUTATED | 6 | 10 | 11 | 13
AMP PEAK 19(XQ28) WILD-TYPE | 18 | 3 | 6 | 10

Figure S81. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.055

Table S82. Gene #19: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
AMP PEAK 19(XQ28) MUTATED | 8 | 14 | 1 | 17
AMP PEAK 19(XQ28) WILD-TYPE | 15 | 9 | 6 | 7

Figure S82. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.11

Table S83. Gene #19: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
AMP PEAK 19(XQ28) MUTATED | 18 | 17 | 4
AMP PEAK 19(XQ28) WILD-TYPE | 21 | 7 | 10

Figure S83. Get High-res Image Gene #19: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.086

Table S84. Gene #20: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 1(1P36.23) MUTATED | 17 | 5 | 8 | 8
DEL PEAK 1(1P36.23) WILD-TYPE | 19 | 21 | 8 | 4

Figure S84. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.032

Table S85. Gene #20: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 1(1P36.23) MUTATED | 13 | 5 | 10 | 2 | 4
DEL PEAK 1(1P36.23) WILD-TYPE | 5 | 6 | 10 | 16 | 7

Figure S85. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00364 (Fisher's exact test), Q value = 0.029

Table S86. Gene #20: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 1(1P36.23) MUTATED | 16 | 9 | 0 | 8
DEL PEAK 1(1P36.23) WILD-TYPE | 7 | 14 | 7 | 16

Figure S86. Get High-res Image Gene #20: 'del_1p36.23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.065

Table S87. Gene #21: 'del_1q43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 2(1Q43) MUTATED | 4 | 3 | 5 | 6
DEL PEAK 2(1Q43) WILD-TYPE | 32 | 23 | 11 | 6

Figure S87. Get High-res Image Gene #21: 'del_1q43' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q43' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.14

Table S88. Gene #21: 'del_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 2(1Q43) MUTATED | 2 | 0 | 8 | 2 | 3
DEL PEAK 2(1Q43) WILD-TYPE | 16 | 11 | 12 | 16 | 8

Figure S88. Get High-res Image Gene #21: 'del_1q43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.13

Table S89. Gene #22: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 3(2Q22.1) MUTATED | 5 | 3 | 4 | 6
DEL PEAK 3(2Q22.1) WILD-TYPE | 31 | 23 | 12 | 6

Figure S89. Get High-res Image Gene #22: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00362 (Fisher's exact test), Q value = 0.029

Table S90. Gene #22: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 3(2Q22.1) MUTATED | 1 | 0 | 8 | 2 | 5
DEL PEAK 3(2Q22.1) WILD-TYPE | 17 | 11 | 12 | 16 | 6

Figure S90. Get High-res Image Gene #22: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.042

Table S91. Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 4(2Q37.3) MUTATED | 5 | 3 | 7 | 6
DEL PEAK 4(2Q37.3) WILD-TYPE | 31 | 23 | 9 | 6

Figure S91. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.098

Table S92. Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 4(2Q37.3) MUTATED | 4 | 0 | 8 | 2 | 5
DEL PEAK 4(2Q37.3) WILD-TYPE | 14 | 11 | 12 | 16 | 6

Figure S92. Get High-res Image Gene #23: 'del_2q37.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.14

Table S93. Gene #24: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 5(3Q13.31) MUTATED | 6 | 1 | 10 | 3 | 1
DEL PEAK 5(3Q13.31) WILD-TYPE | 12 | 10 | 10 | 15 | 10

Figure S93. Get High-res Image Gene #24: 'del_3q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 0.13

Table S94. Gene #24: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 5(3Q13.31) MUTATED | 7 | 10 | 2 | 2
DEL PEAK 5(3Q13.31) WILD-TYPE | 16 | 13 | 5 | 22

Figure S94. Get High-res Image Gene #24: 'del_3q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.014

Table S95. Gene #25: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 6(4Q34.3) MUTATED | 17 | 3 | 5 | 0
DEL PEAK 6(4Q34.3) WILD-TYPE | 19 | 23 | 11 | 12

Figure S95. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.086

Table S96. Gene #25: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
DEL PEAK 6(4Q34.3) MUTATED | 11 | 2 | 3 | 2
DEL PEAK 6(4Q34.3) WILD-TYPE | 13 | 11 | 14 | 21

Figure S96. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.13

Table S97. Gene #25: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 6(4Q34.3) MUTATED | 10 | 5 | 1 | 2
DEL PEAK 6(4Q34.3) WILD-TYPE | 13 | 18 | 6 | 22

Figure S97. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.12

Table S98. Gene #25: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
DEL PEAK 6(4Q34.3) MUTATED | 11 | 6 | 2
DEL PEAK 6(4Q34.3) WILD-TYPE | 25 | 10 | 24

Figure S98. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.13

Table S99. Gene #25: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
DEL PEAK 6(4Q34.3) MUTATED | 2 | 7 | 0 | 9 | 1
DEL PEAK 6(4Q34.3) WILD-TYPE | 14 | 20 | 11 | 11 | 3

Figure S99. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0019

Table S100. Gene #25: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 6(4Q34.3) MUTATED | 4 | 13 | 2
DEL PEAK 6(4Q34.3) WILD-TYPE | 24 | 9 | 25

Figure S100. Get High-res Image Gene #25: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.016

Table S101. Gene #26: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 7(4Q34.3) MUTATED | 15 | 2 | 9 | 2
DEL PEAK 7(4Q34.3) WILD-TYPE | 21 | 24 | 7 | 10

Figure S101. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00494 (Fisher's exact test), Q value = 0.037

Table S102. Gene #26: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 7(4Q34.3) MUTATED | 11 | 0 | 7 | 3 | 3
DEL PEAK 7(4Q34.3) WILD-TYPE | 7 | 11 | 13 | 15 | 8

Figure S102. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0027

Table S103. Gene #26: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 7(4Q34.3) MUTATED | 5 | 15 | 4
DEL PEAK 7(4Q34.3) WILD-TYPE | 23 | 7 | 23

Figure S103. Get High-res Image Gene #26: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.04

Table S104. Gene #27: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 8(4Q35.1) MUTATED | 17 | 4 | 8 | 1
DEL PEAK 8(4Q35.1) WILD-TYPE | 19 | 22 | 8 | 11

Figure S104. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.058

Table S105. Gene #27: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 8(4Q35.1) MUTATED | 11 | 1 | 8 | 3 | 2
DEL PEAK 8(4Q35.1) WILD-TYPE | 7 | 10 | 12 | 15 | 9

Figure S105. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.13

Table S106. Gene #27: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 8(4Q35.1) MUTATED | 10 | 10 | 1 | 3
DEL PEAK 8(4Q35.1) WILD-TYPE | 13 | 13 | 6 | 21

Figure S106. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.012

Table S107. Gene #27: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 8(4Q35.1) MUTATED | 5 | 14 | 5
DEL PEAK 8(4Q35.1) WILD-TYPE | 23 | 8 | 22

Figure S107. Get High-res Image Gene #27: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.13

Table S108. Gene #30: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 11(7Q36.3) MUTATED | 8 | 0 | 2 | 1
DEL PEAK 11(7Q36.3) WILD-TYPE | 28 | 26 | 14 | 11

Figure S108. Get High-res Image Gene #30: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 0.00907 (Fisher's exact test), Q value = 0.05

Table S109. Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 12(9P23) MUTATED | 16 | 2 | 4 | 2
DEL PEAK 12(9P23) WILD-TYPE | 20 | 24 | 12 | 10

Figure S109. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00828 (Fisher's exact test), Q value = 0.048

Table S110. Gene #31: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 12(9P23) MUTATED | 11 | 2 | 2 | 4 | 2
DEL PEAK 12(9P23) WILD-TYPE | 7 | 9 | 18 | 14 | 9

Figure S110. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0013

Table S111. Gene #31: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
DEL PEAK 12(9P23) MUTATED | 15 | 1 | 4 | 1
DEL PEAK 12(9P23) WILD-TYPE | 9 | 12 | 13 | 22

Figure S111. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.014

Table S112. Gene #31: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 12(9P23) MUTATED | 13 | 4 | 2 | 2
DEL PEAK 12(9P23) WILD-TYPE | 10 | 19 | 5 | 22

Figure S112. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.046

Table S113. Gene #31: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
DEL PEAK 12(9P23) MUTATED | 11 | 8 | 2
DEL PEAK 12(9P23) WILD-TYPE | 25 | 8 | 24

Figure S113. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.048

Table S114. Gene #31: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 12(9P23) MUTATED | 6 | 11 | 3
DEL PEAK 12(9P23) WILD-TYPE | 22 | 11 | 24

Figure S114. Get High-res Image Gene #31: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.0069 (Fisher's exact test), Q value = 0.043

Table S115. Gene #32: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 13(9P21.3) MUTATED | 18 | 3 | 4 | 2
DEL PEAK 13(9P21.3) WILD-TYPE | 18 | 23 | 12 | 10

Figure S115. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.029

Table S116. Gene #32: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 13(9P21.3) MUTATED | 12 | 3 | 2 | 5 | 2
DEL PEAK 13(9P21.3) WILD-TYPE | 6 | 8 | 18 | 13 | 9

Figure S116. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00035

Table S117. Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
DEL PEAK 13(9P21.3) MUTATED | 17 | 1 | 4 | 2
DEL PEAK 13(9P21.3) WILD-TYPE | 7 | 12 | 13 | 21

Figure S117. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0061

Table S118. Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 13(9P21.3) MUTATED | 15 | 4 | 2 | 3
DEL PEAK 13(9P21.3) WILD-TYPE | 8 | 19 | 5 | 21

Figure S118. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.073

Table S119. Gene #32: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
DEL PEAK 13(9P21.3) MUTATED | 13 | 8 | 3
DEL PEAK 13(9P21.3) WILD-TYPE | 23 | 8 | 23

Figure S119. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00934 (Fisher's exact test), Q value = 0.05

Table S120. Gene #32: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 13(9P21.3) MUTATED | 7 | 12 | 4
DEL PEAK 13(9P21.3) WILD-TYPE | 21 | 10 | 23

Figure S120. Get High-res Image Gene #32: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.00767 (Fisher's exact test), Q value = 0.046

Table S121. Gene #34: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 15(11P15.5) MUTATED | 7 | 5 | 7 | 8
DEL PEAK 15(11P15.5) WILD-TYPE | 29 | 21 | 9 | 4

Figure S121. Get High-res Image Gene #34: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.082

Table S122. Gene #34: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 15(11P15.5) MUTATED | 4 | 3 | 12 | 2 | 4
DEL PEAK 15(11P15.5) WILD-TYPE | 14 | 8 | 8 | 16 | 7

Figure S122. Get High-res Image Gene #34: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.12

Table S123. Gene #34: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 15(11P15.5) MUTATED | 4 | 11 | 0 | 9
DEL PEAK 15(11P15.5) WILD-TYPE | 19 | 12 | 7 | 15

Figure S123. Get High-res Image Gene #34: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.081

Table S124. Gene #35: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 16(11Q14.1) MUTATED | 9 | 3 | 6 | 7
DEL PEAK 16(11Q14.1) WILD-TYPE | 27 | 23 | 10 | 5

Figure S124. Get High-res Image Gene #35: 'del_11q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 0.00681 (Fisher's exact test), Q value = 0.043

Table S125. Gene #35: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 16(11Q14.1) MUTATED | 2 | 1 | 11 | 3 | 5
DEL PEAK 16(11Q14.1) WILD-TYPE | 16 | 10 | 9 | 15 | 6

Figure S125. Get High-res Image Gene #35: 'del_11q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.012

Table S126. Gene #36: 'del_12q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 17(12Q14.2) MUTATED | 2 | 0 | 3 | 0
DEL PEAK 17(12Q14.2) WILD-TYPE | 21 | 23 | 4 | 24

Figure S126. Get High-res Image Gene #36: 'del_12q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.028

Table S127. Gene #37: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 18(13Q14.2) MUTATED | 21 | 5 | 7 | 9
DEL PEAK 18(13Q14.2) WILD-TYPE | 15 | 21 | 9 | 3

Figure S127. Get High-res Image Gene #37: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q21.2' versus 'CN_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.082

Table S128. Gene #38: 'del_14q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 19(14Q21.2) MUTATED | 7 | 3 | 3 | 7
DEL PEAK 19(14Q21.2) WILD-TYPE | 29 | 23 | 13 | 5

Figure S128. Get High-res Image Gene #38: 'del_14q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00841 (Fisher's exact test), Q value = 0.048

Table S129. Gene #39: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 20(16P13.3) MUTATED | 2 | 2 | 3 | 0
DEL PEAK 20(16P13.3) WILD-TYPE | 21 | 21 | 4 | 24

Figure S129. Get High-res Image Gene #39: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.091

Table S130. Gene #39: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
DEL PEAK 20(16P13.3) MUTATED | 3 | 4 | 0
DEL PEAK 20(16P13.3) WILD-TYPE | 33 | 12 | 26

Figure S130. Get High-res Image Gene #39: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.082

Table S131. Gene #39: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 20(16P13.3) MUTATED | 2 | 5 | 0
DEL PEAK 20(16P13.3) WILD-TYPE | 26 | 17 | 27

Figure S131. Get High-res Image Gene #39: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.048

Table S132. Gene #40: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 21(16Q23.1) MUTATED | 9 | 0 | 2 | 0
DEL PEAK 21(16Q23.1) WILD-TYPE | 27 | 26 | 14 | 12

Figure S132. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.13

Table S133. Gene #40: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
DEL PEAK 21(16Q23.1) MUTATED | 6 | 1 | 0 | 1
DEL PEAK 21(16Q23.1) WILD-TYPE | 18 | 12 | 17 | 22

Figure S133. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.054

Table S134. Gene #40: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 21(16Q23.1) MUTATED | 5 | 1 | 2 | 0
DEL PEAK 21(16Q23.1) WILD-TYPE | 18 | 22 | 5 | 24

Figure S134. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.055

Table S135. Gene #40: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 21(16Q23.1) MUTATED | 1 | 6 | 1
DEL PEAK 21(16Q23.1) WILD-TYPE | 27 | 16 | 26

Figure S135. Get High-res Image Gene #40: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.068

Table S136. Gene #41: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 22(17Q11.2) MUTATED | 12 | 3 | 8 | 1
DEL PEAK 22(17Q11.2) WILD-TYPE | 24 | 23 | 8 | 11

Figure S136. Get High-res Image Gene #41: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.037

Table S137. Gene #41: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 22(17Q11.2) MUTATED | 7 | 0 | 11 | 4 | 1
DEL PEAK 22(17Q11.2) WILD-TYPE | 11 | 11 | 9 | 14 | 10

Figure S137. Get High-res Image Gene #41: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.077

Table S138. Gene #41: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
DEL PEAK 22(17Q11.2) MUTATED | 4 | 7 | 0 | 11 | 1
DEL PEAK 22(17Q11.2) WILD-TYPE | 12 | 20 | 11 | 9 | 3

Figure S138. Get High-res Image Gene #41: 'del_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.032

Table S139. Gene #42: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 23(17Q21.31) MUTATED | 13 | 3 | 9 | 1
DEL PEAK 23(17Q21.31) WILD-TYPE | 23 | 23 | 7 | 11

Figure S139. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 0.00939 (Fisher's exact test), Q value = 0.05

Table S140. Gene #42: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 23(17Q21.31) MUTATED | 7 | 1 | 12 | 4 | 1
DEL PEAK 23(17Q21.31) WILD-TYPE | 11 | 10 | 8 | 14 | 10

Figure S140. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.14

Table S141. Gene #42: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 23(17Q21.31) MUTATED | 9 | 11 | 2 | 3
DEL PEAK 23(17Q21.31) WILD-TYPE | 14 | 12 | 5 | 21

Figure S141. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.12

Table S142. Gene #42: 'del_17q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
DEL PEAK 23(17Q21.31) MUTATED | 17 | 3 | 5
DEL PEAK 23(17Q21.31) WILD-TYPE | 19 | 13 | 21

Figure S142. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00522 (Fisher's exact test), Q value = 0.038

Table S143. Gene #42: 'del_17q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
DEL PEAK 23(17Q21.31) MUTATED | 6 | 6 | 0 | 12 | 1
DEL PEAK 23(17Q21.31) WILD-TYPE | 10 | 21 | 11 | 8 | 3

Figure S143. Get High-res Image Gene #42: 'del_17q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17q24.2' versus 'CN_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.018

Table S144. Gene #43: 'del_17q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 24(17Q24.2) MUTATED | 10 | 3 | 10 | 1
DEL PEAK 24(17Q24.2) WILD-TYPE | 26 | 23 | 6 | 11

Figure S144. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.2' versus 'METHLYATION_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.067

Table S145. Gene #43: 'del_17q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
DEL PEAK 24(17Q24.2) MUTATED | 6 | 2 | 12 | 3 | 1
DEL PEAK 24(17Q24.2) WILD-TYPE | 12 | 9 | 8 | 15 | 10

Figure S145. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.13

Table S146. Gene #43: 'del_17q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 24(17Q24.2) MUTATED | 8 | 11 | 1 | 3
DEL PEAK 24(17Q24.2) WILD-TYPE | 15 | 12 | 6 | 21

Figure S146. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.098

Table S147. Gene #43: 'del_17q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
DEL PEAK 24(17Q24.2) MUTATED | 6 | 7 | 0 | 8 | 3
DEL PEAK 24(17Q24.2) WILD-TYPE | 10 | 20 | 11 | 12 | 1

Figure S147. Get High-res Image Gene #43: 'del_17q24.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.11

Table S148. Gene #44: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 25(18Q21.2) MUTATED | 16 | 5 | 7 | 8
DEL PEAK 25(18Q21.2) WILD-TYPE | 20 | 21 | 9 | 4

Figure S148. Get High-res Image Gene #44: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.00472 (Fisher's exact test), Q value = 0.036

Table S149. Gene #45: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 26(20P12.1) MUTATED | 10 | 0 | 2 | 0
DEL PEAK 26(20P12.1) WILD-TYPE | 26 | 26 | 14 | 12

Figure S149. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.13

Table S150. Gene #45: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
DEL PEAK 26(20P12.1) MUTATED | 6 | 1 | 2 | 0
DEL PEAK 26(20P12.1) WILD-TYPE | 18 | 12 | 15 | 23

Figure S150. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.1

Table S151. Gene #45: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
DEL PEAK 26(20P12.1) MUTATED | 6 | 2 | 1 | 0
DEL PEAK 26(20P12.1) WILD-TYPE | 17 | 21 | 6 | 24

Figure S151. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.042

Table S152. Gene #45: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
DEL PEAK 26(20P12.1) MUTATED | 4 | 5 | 0
DEL PEAK 26(20P12.1) WILD-TYPE | 32 | 11 | 26

Figure S152. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.016

Table S153. Gene #45: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
DEL PEAK 26(20P12.1) MUTATED | 2 | 7 | 0
DEL PEAK 26(20P12.1) WILD-TYPE | 26 | 15 | 27

Figure S153. Get High-res Image Gene #45: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q12.1' versus 'CN_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.032

Table S154. Gene #46: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
DEL PEAK 27(22Q12.1) MUTATED | 22 | 7 | 12 | 9
DEL PEAK 27(22Q12.1) WILD-TYPE | 14 | 19 | 4 | 3

Figure S154. Get High-res Image Gene #46: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

- Copy number data file = all_lesions.txt from GISTIC pipeline

- Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/15081748/transformed.cor.cli.txt

- Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/15087341/ACC-TP.transferedmergedcluster.txt

- Number of patients = 90

- Number of significantly focal cnvs = 46

- Number of molecular subtypes = 10

- Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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